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Sample GSM28547 Query DataSets for GSM28547
Status Public on Feb 09, 2005
Title LPS 6hr Rat #4 flip
Sample type RNA
 
Channel 1
Source name LPS 6hr Rat #4
Organism Rattus norvegicus
Extracted molecule total RNA
 
Channel 2
Source name Control Pool 6hr LPS
Organism Rattus norvegicus
Extracted molecule total RNA
 
 
Description LPS 6hr Rat #4 flip
 
Submission date Aug 10, 2004
Last update date May 27, 2005
Contact name Rick David Fannin
E-mail(s) fannin@niehs.nih.gov
Phone 919-541-0992
Fax 919-541-1506
URL http://www.niehs.nih.gov/nct/
Organization name The National Institute of Environmental Health Sciences
Department Office of the Director
Lab National Center for Toxicogenomics/Toxicology-Pathology Working
Street address 111 T.W. Alexander Drive
City Durham
State/province NC
ZIP/Postal code 27709
Country USA
 
Platform ID GPL1344
Series (1)
GSE1658 LPS Blood Time course

Data table header descriptions
ID_REF
SR_top Bonding box location in Red channel image coordinates - (top) (SR -- Sample in Red channel)
SR_left Bonding box location in Red channel image coordinates - (left) (SR -- Sample in Red channel)
SR_bottom Bonding box location in Red channel image coordinates - (bottom) (SR -- Sample in Red channel)
SR_right Bonding box location in Red channel image coordinates - (right) (SR -- Sample in Red channel)
SR_T. Int. Total Intensity - Sum of all pixel gray-levels within the target area. No data trimming is performed here.
SR_Mean Mean Intensity - Average of all pixel gray-leves within the target area, after trimming top and bottom 5%
SR_S.Dev Std. Dev. Of intensity - Std. Dev. Of signal intensity. Derived along with mean intensity
SR_SNR Signal-to-Noise Ratio. It is roughly the ratio of mean signal intensity to the local background variation.
SR_iQuality The measurement quality. Summarized from Area, Background, Consistency, and Saturation. From 0 (bad) to 1 (good)
SR_bkMean Mean background Intensity
SR_bkDev Std. Dev. Of background intensity
SG_top Bonding box location in Green channel image coordinates - (top) (SG -- Sample in Green channel)
SG_left Bonding box location in Green channel image coordinates - (left) (SG -- Sample in Green channel)
SG_bottom Bonding box location in Green channel image coordinates - (bottom) (SG -- Sample in Green channel)
SG_right Bonding box location in Green channel image coordinates - (right) (SG -- Sample in Green channel)
SG_T. Int. Total Intensity - Sum of all pixel gray-levels within the target area. No data trimming is performed here.
SG_Mean Mean Intensity - Average of all pixel gray-leves within the target area, after trimming top and bottom 5%
SG_S.Dev Std. Dev. Of intensity - Std. Dev. Of signal intensity. Derived along with mean intensity
SG_SNR Signal-to-Noise Ratio. It is roughly the ratio of mean signal intensity to the local background variation.
SG_iQuality The measurement quality. Summarized from Area, Background, Consistency, and Saturation. From 0 (bad) to 1 (good)
SG_bkMean Mean background Intensity
SG_bkDev Std. Dev. Of background intensity
unionArea Union Area - the detected target area. All calculations are based on this region
propArea Proportional area relatively to the mask size.
VALUE log ratio (log2 of PRE_VALUE)
rQuality Ratio measurement quality (including all intensity measurement quality, plus the signal-to-noise-ratio requirement).
confLevel Confidence Level, typically set at 99%
lowerLimit Lower Limit of confidence interval for cal. Ratio
upperLimit Upper Limit of confidence interval for cal. Ratio
M Magnitude parameter for channel compensation
CV Coefficient of variation of the intensity
Flag User flagged. 0 - deleted spot by user, 1 - good spot
HKFlag House Keeping flag
GelBand Number of bands
PRE_VALUE Calibrated ratio, (or normalized ratio)

Data table
ID_REF SR_top SR_left SR_bottom SR_right SR_T. Int. SR_Mean SR_S.Dev SR_SNR SR_iQuality SR_bkMean SR_bkDev SG_top SG_left SG_bottom SG_right SG_T. Int. SG_Mean SG_S.Dev SG_SNR SG_iQuality SG_bkMean SG_bkDev unionArea propArea VALUE rQuality confLevel lowerLimit upperLimit M CV Flag HKFlag GelBand PRE_VALUE
1 649 155 676 182 111058 162.1 119.9 11.1 1 466.1 10.6 649 155 676 182 104387 194.7 109.3 20.7 1 399.5 5.9 175 0.9259 0.1714633 1 99 0.8141 1.2283 0.7394 0.056 1 0 1 1.1262
2 645 605 672 632 51770 71.9 74 5.1 0.3511 452 9.8 645 605 672 632 40766 22.3 14 2.3 1 398.1 6.9 97 0.6831 2.1262133 0.2 99 0.8141 1.2283 0.7394 0.056 1 0 1 4.3657
3 645 1059 672 1086 153185 494.7 323.9 36.9 1 453.1 8.8 645 1059 672 1086 154421 564 380.1 68.2 1 392.7 5 157 1 0.2464693 1 99 0.8141 1.2283 0.7394 0.056 1 0 1 1.1863
4 641 1509 668 1536 282669 1102.3 454.2 79.6 1 458 9.1 641 1509 668 1536 306535 1282.5 559.6 129.5 1 398.6 6.8 177 1 0.2172313 1 99 0.8141 1.2283 0.7394 0.056 1 0 1 1.1625
5 649 211 676 238 312452 1180.1 834.6 80 1 457.3 10.7 649 211 676 238 353663 1452 1039.7 151.1 1 399.3 6.2 189 1 0.1365853 1 99 0.8141 1.2283 0.7394 0.056 1 0 1 1.0993
6 645 661 672 688 181167 821.8 364.6 58.6 1 451.1 9.7 645 661 672 688 201703 1018.4 447 107.9 1 397.6 6.6 142 1 0.1261803 1 99 0.8141 1.2283 0.7394 0.056 1 0 1 1.0914
7 645 1115 672 1142 143741 526 348.8 38.6 1 450.4 9.2 645 1115 672 1142 146470 601.5 401.1 70 1 393.3 5.5 146 0.9299 0.2422063 1 99 0.8141 1.2283 0.7394 0.056 1 0 1 1.1828
8 641 1565 668 1592 219051 780 172.8 54.5 1 457.6 9.8 641 1565 668 1592 240683 965.9 220.2 94.6 1 398.9 7.2 177 1 0.1271053 1 99 0.8141 1.2283 0.7394 0.056 1 0 1 1.0921
9 649 267 676 294 512416 2232.2 1369.5 152.5 1 457.7 10.6 649 267 676 294 516618 2300.7 1420.6 219.8 1 402.6 7.5 189 1 0.3919883 1 99 0.8141 1.2283 0.7394 0.056 1 0 1 1.3122
10 645 717 672 744 172360 762.1 382.7 55 1 454.6 9.5 645 717 672 744 188291 928.6 485.6 97.5 1 396.7 6.7 142 1 0.1505603 1 99 0.8141 1.2283 0.7394 0.056 1 0 1 1.11
11 645 1171 672 1198 313932 1537 647.9 112.6 1 451.1 9.2 645 1171 672 1198 365001 1914.3 860.3 213.5 1 394.6 6.1 157 1 0.1188913 1 99 0.8141 1.2283 0.7394 0.056 1 0 1 1.0859
12 641 1621 668 1648 227844 835.3 437.9 61.9 1 456.5 8.6 641 1621 668 1648 243133 973.9 521.3 92.6 1 401.5 7.6 177 1 0.2141253 1 99 0.8141 1.2283 0.7394 0.056 1 0 1 1.16
13 648 323 675 350 213380 675.5 371.9 45.1 1 453.8 11 648 323 675 350 249617 926.5 529.9 102.2 1 396 5.4 189 1 -0.0201943 1 99 0.8141 1.2283 0.7394 0.056 1 0 1 0.9861
14 644 773 671 800 281325 1456.4 640.8 101 1 454.7 10.3 644 773 671 800 325035 1820 802 192.9 1 398.2 6.6 142 1 0.1141003 1 99 0.8141 1.2283 0.7394 0.056 1 0 1 1.0823
15 644 1227 671 1254 193650 813.6 408.7 34.4 1 449.9 21.4 644 1227 671 1254 212516 993.5 508.8 94.7 1 393.8 8.1 154 0.9809 0.1473073 1 99 0.8141 1.2283 0.7394 0.056 1 0 1 1.1075
16 640 1677 667 1704 216471 751.3 253.8 52.6 1 455.6 9.8 640 1677 667 1704 240733 944.4 309.9 94.8 1 401.6 6.8 177 1 0.1056783 1 99 0.8141 1.2283 0.7394 0.056 1 0 1 1.076
17 648 378 675 405 1052037 5101.4 2901.5 352.9 1 454 10.3 648 378 675 405 1508208 7523.7 4382 741.7 1 398.7 7 189 1 -0.1248493 1 99 0.8141 1.2283 0.7394 0.056 1 0 1 0.9171
18 644 828 671 855 150105 585.1 267 40.7 1 456.2 10.3 644 828 671 855 154958 670 313.4 67.6 1 399.2 7.3 142 1 0.2400093 1 99 0.8141 1.2283 0.7394 0.056 1 0 1 1.181
19 644 1282 671 1309 93413 295.7 157.1 13.8 1 452.7 18.9 644 1282 671 1309 93151 349 182 36.1 1 394.5 7 125 0.7962 0.1964813 1 99 0.8141 1.2283 0.7394 0.056 1 0 1 1.1459
20 640 1732 667 1759 162960 517.3 336 23.6 1 460.5 19.3 640 1732 667 1759 186804 717.5 484.7 66.5 1 401.1 8 164 0.9266 -0.0363783 1 99 0.8141 1.2283 0.7394 0.056 1 0 1 0.9751

Total number of rows: 7200

Table truncated, full table size 1245 Kbytes.




Supplementary file Size Download File type/resource
GSM28547.TIF.gz 11.7 Mb (ftp)(http) TIFF

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